# Paired Samples in Lima Voom for Bulk RNAseq

**URL:** <https://help.galaxyproject.org/t/paired-samples-in-lima-voom-for-bulk-rnaseq/4258>\
**Category:** usegalaxy.org support\
**Created:** [August 8, 2020, 6:54pm UTC](https://help.galaxyproject.org/t/paired-samples-in-lima-voom-for-bulk-rnaseq/4258 "2020-08-08T18:54:22Z")\
**Posts on this page:** 1\
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**Author:** ![TXP](https://avatars.discourse-cdn.com/v4/letter/t/8dc957/32.png) [@TXP](https://help.galaxyproject.org/u/TXP)\
**Post date:** [August 8, 2020, 6:54pm UTC](https://help.galaxyproject.org/t/paired-samples-in-lima-voom-for-bulk-rnaseq/4258/1 "2020-08-08T18:54:22Z")

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Hi,

I am not sure if I am suppose to ask this question here or not. Seems like most topics are about server/tool errors. If I am in the wrong place, please let me know where I need to go.

I have been trying to analyze Bulk-RNAseq data following the Reads to Count tutorial by Maria Doyle et al. Everything went well, but the results are a bit funky. I believe it is because my data comes from 3 different cell types. The conditons are as follows: Cell1, Cell2, Cell3 and Cell1 treated, Cell2 treated, and Cell3 treated. I am only interested in the “treated” effect, rather than the variation within each cell type. Is there a way to “pair” the differential expression to between the cell1 and cell1 treated, but still compare the untreated to treated as a groups?

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_[View the full topic](https://help.galaxyproject.org/t/paired-samples-in-lima-voom-for-bulk-rnaseq/4258)._